From bdb62e8046c9e7041f2a7881cac16742b5857b94 Mon Sep 17 00:00:00 2001 From: rowanc1 Date: Sat, 17 May 2014 22:10:31 -0700 Subject: [PATCH] Documentation updates --- docs/api_Maps.rst | 19 +++++----- docs/api_Solver.rst | 7 +++- docs/api_bigPicture.rst | 17 +++++++++ docs/api_installing.rst | 77 +++++++++++++++++++++++++++++++++++++++++ docs/api_license.rst | 10 ++++-- docs/index.rst | 62 ++++++++++++++++++--------------- 6 files changed, 153 insertions(+), 39 deletions(-) create mode 100644 docs/api_bigPicture.rst create mode 100644 docs/api_installing.rst diff --git a/docs/api_Maps.rst b/docs/api_Maps.rst index b590203c..abd35838 100644 --- a/docs/api_Maps.rst +++ b/docs/api_Maps.rst @@ -4,6 +4,9 @@ SimPEG Maps *********** +Thats not a map...?! +==================== + A SimPEG Map operates on a vector and transforms it to another space. We will use an example commonly applied in electromagnetics (EM) of the log-conductivity model. @@ -70,14 +73,6 @@ When these are used in the inverse problem, this is extremely important!! expMap.test(m, plotIt=True) -The API -======= - -.. autoclass:: SimPEG.Maps.IdentityMap - :members: - :undoc-members: - - Combining Maps ============== @@ -127,6 +122,14 @@ Just to be sure that the derivative is correct, you should always run the test on the mapping that you create. +The API +======= + +.. autoclass:: SimPEG.Maps.IdentityMap + :members: + :undoc-members: + + Common Maps =========== diff --git a/docs/api_Solver.rst b/docs/api_Solver.rst index 9909b65e..d96bd9b2 100644 --- a/docs/api_Solver.rst +++ b/docs/api_Solver.rst @@ -4,6 +4,9 @@ Solver ****** +BYOS +==== + The numerical linear algebra solver that you use will ultimately be the bottleneck of your large scale inversion. To be the most flexible, SimPEG provides wrappers rather than a comprehensive set of solvers (i.e. BYOS). @@ -34,7 +37,9 @@ To wrap up solvers in scipy.sparse.linalg it takes one line of code:: .. seealso:: - https://github.com/rowanc1/pymatsolver + - https://bitbucket.org/petsc/petsc4py + - https://github.com/bfroehle/pymumps + - https://github.com/rowanc1/pymatsolver The API diff --git a/docs/api_bigPicture.rst b/docs/api_bigPicture.rst new file mode 100644 index 00000000..a712dae3 --- /dev/null +++ b/docs/api_bigPicture.rst @@ -0,0 +1,17 @@ +.. _api_license: + +Why SimPEG? +*********** + + +The Big Picture +=============== + +.. image:: simpeg-framework.png + :width: 400 px + :alt: Framework + :align: center + + +Explaining The Big Picture +========================== diff --git a/docs/api_installing.rst b/docs/api_installing.rst new file mode 100644 index 00000000..ede400d0 --- /dev/null +++ b/docs/api_installing.rst @@ -0,0 +1,77 @@ +.. _api_installing: + +Installation +************ + +Dependencies +============ + +- Python 2.7 +- NumPy 1.8 (or greater) +- SciPy 0.13 (or greater) +- matplotlib 1.3 (or greater) +- Cython 0.20 (or greater) + +Installing Python +================= + +Python is available on all major operating systems, but if you are getting started with python +it is best to use a package manager such as +`Continuum Anaconda `_ or +`Enthought Canopy `_. +You can download the package manager and use it to install the dependencies above. + + +Installing SimPEG +================= + +SimPEG is not **yet** on pip. + +Installing from Source +---------------------- + +First (you need git):: + + git clone https://github.com/simpeg/simpeg + +Second (from the root of the simpeg repository):: + + python setup.py install + + +Useful Links +============ +An enormous amount of information (including tutorials and examples) can be found on the official websites of the packages + +* `Python Website `_ +* `Numpy Website `_ +* `SciPy Website `_ +* `Matplotlib `_ + +Python for scientific computing +------------------------------- + +* `Python for Scientists `_ Links to commonly used packages, Matlab to Python comparison +* `Python Wiki `_ Lists packages and resources for scientific computing in Python + +Numpy and Matlab +---------------- + +* `NumPy for Matlab Users `_ +* `Python vs Matlab `_ + +Lessons in Python +----------------- + +* `Software Carpentry `_ +* `Introduction to NumPy and Matplotlib `_ + +Editing Python +-------------- + +There are numerous ways to edit and test Python (see `PythonWiki `_ for an overview) and in our group at least the following options are being used: + +* `Sublime `_ +* `iPython Notebook `_ +* `iPython `_ +* `Enthought Canopy `_ diff --git a/docs/api_license.rst b/docs/api_license.rst index eab8d73e..b8f2d439 100644 --- a/docs/api_license.rst +++ b/docs/api_license.rst @@ -1,11 +1,17 @@ .. _api_license: License -======= +******* .. include:: ../LICENSE Authors -======= +******* .. include:: ../AUTHORS.rst + + +Projects Using SimPEG +********************* + +.. include:: ../PROJECTS.rst diff --git a/docs/index.rst b/docs/index.rst index 22709033..88cc4ee1 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -1,30 +1,47 @@ +SimPEG Documentation +******************** + .. image:: simpeg-logo.png :width: 300 px :alt: SimPEG :align: center -Simulation and Parameter Estimation in Geophysics -************************************************* +SimPEG: Simulation and Parameter Estimation in Geophysics -SimPEG is a python package for simulation and gradient -based parameter estimation in the context of geoscience applications. - -The vision is to create a package for finite volume simulation and parameter estimation with +SimPEG is a framework and a collection of tools that aid in the development of +large-scale geophysical inversion codes. +The vision is to create a modular and extensible package for +finite volume simulation and parameter estimation with applications to geophysical imaging and subsurface flow. To enable these goals, this package has the following features: -- is modular with respect to discretization, physics, optimization, and regularization +- is modular with respect to ... everything! - is built with the (large-scale) inverse problem in mind - provides a framework for geophysical and hydrogeologic problems - supports 1D, 2D and 3D problems +- provides a set of commonly used visualization utilities -.. image:: simpeg-framework.png - :width: 400 px - :alt: Framework - :align: center -Meshing & Operators -******************* +About SimPEG +************ + +.. toctree:: + :maxdepth: 2 + + api_bigPicture + api_license + + +Getting Started with SimPEG +*************************** + +.. toctree:: + :maxdepth: 2 + + api_installing + +Discretization +************** .. toctree:: :maxdepth: 3 @@ -60,17 +77,12 @@ Utility Codes api_Solver api_Maps api_Utils - - -Miscellaneous -************* - -.. toctree:: - :maxdepth: 2 - - api_license api_Tests + +Developer's Documentation +************************* + * Travis-CI Testing .. image:: https://travis-ci.org/simpeg/simpeg.svg?branch=master :target: https://travis-ci.org/simpeg/simpeg @@ -84,12 +96,6 @@ Miscellaneous :align: center - -Projects Using SimPEG -********************* - -.. include:: ../PROJECTS.rst - Project Index & Search **********************